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@triplets = unpack ('(a3)*', $line);

# throw away trailing crud
pop @triplets if $triplets[-1] !~ /.../;

my $line      = 'atccatccctttaat';
my @triplets  = unpack( '(a3)*', $line);
...
pop @triplets  if $triplets[-1]  !~ /.../;
pop @triplets2 if $triplets2[-1] !~ /.../;
pop @triplets3 if $triplets3[-1] !~ /.../;

my @triplets = unpack("x${skip}(a3)*", $line);
pop @triplets if $triplets[-1]  !~ /.../;

--
@/=map{[/./g]}qw/.h_nJ Xapou cets krht ele_ r_ra/;
map{y/X_/\n /;print}map{pop@$_}@/for@/